Index

B

BaseModel (class in mimic.model_simulate.base_model)

C

check_params() (mimic.model_simulate.base_model.BaseModel method) choose_denom() (in module mimic.model_infer.cLV) compare_params() (in module mimic.utilities.utilities)

CompositionalLotkaVolterra (class in mimic.model_infer.cLV) compute_prediction_error() (in module mimic.model_infer.cLV) compute_rel_abun() (in module mimic.model_infer.cLV) construct_alr() (in module mimic.model_infer.cLV)

D

debug (mimic.model_simulate.base_model.BaseModel property) do_bootstrapping() (in module mimic.model_infer.infer_gMLV_lm)

do_final_fit_Ridge1() (in module mimic.model_infer.infer_gMLV_lm) do_final_fit_Ridge2() (in module mimic.model_infer.infer_gMLV_lm)

E

elastic_net_clv() (in module mimic.model_infer.cLV) estimate_elastic_net_regularizers_cv() (in module mimic.model_infer.cLV)

estimate_relative_abundances() (in module mimic.model_infer.cLV) estimate_ridge_regularizers_cv() (in module mimic.model_infer.cLV)

F

fit() (mimic.model_infer.infer_gMLV_lm.Ridge1 method) (mimic.model_infer.infer_gMLV_lm.Ridge2 method) (mimic.model_infer.multi_penalty_lasso.MultiPenaltyLasso method)

fit_alpha_lasso() (in module mimic.model_infer.infer_gMLV_lm) fit_alpha_MPLasso() (in module mimic.model_infer.multi_penalty_lasso) fit_alpha_Ridge1() (in module mimic.model_infer.infer_gMLV_lm) fit_alpha_Ridge2() (in module mimic.model_infer.infer_gMLV_lm)

G

generate_mvar1_data() (mimic.model_simulate.sim_VAR.sim_VAR method) generate_var1_data() (mimic.model_simulate.sim_VAR.sim_VAR method) get_params() (mimic.model_infer.cLV.CompositionalLotkaVolterra method) (mimic.model_infer.infer_gMLV_lm.Ridge1 method) (mimic.model_infer.infer_gMLV_lm.Ridge2 method) (mimic.model_infer.multi_penalty_lasso.MultiPenaltyLasso method)

get_regularizers() (mimic.model_infer.cLV.CompositionalLotkaVolterra method) gMLV() (in module mimic.model_simulate.sim_gMLV)

I

infer_VAR (class in mimic.model_infer.infer_VAR_bayes)

L

linearise_time_course_metabolites() (in module mimic.model_infer.infer_gMLV_lm) linearize_time_course() (in module mimic.model_infer.infer_gMLV_lm)

linearize_time_course_16S() (in module mimic.model_infer.infer_gMLV_lm) linearize_time_course_16S_u() (in module mimic.model_infer.infer_gMLV_lm) load_data() (mimic.model_simulate.base_model.BaseModel method)

M

make_plot() (mimic.model_simulate.sim_VAR.sim_VAR method) make_plot_overlay() (mimic.model_simulate.sim_VAR.sim_VAR method) make_plot_stacked() (mimic.model_infer.infer_VAR_bayes.infer_VAR method) (mimic.model_simulate.sim_VAR.sim_VAR method) mimic module mimic.model_infer module mimic.model_infer.cLV module mimic.model_infer.infer_gMLV_lm module mimic.model_infer.infer_VAR_bayes module mimic.model_infer.multi_penalty_lasso module mimic.model_simulate module mimic.model_simulate.base_model module mimic.model_simulate.sim_gMLV module

mimic.model_simulate.sim_VAR module mimic.utilities module mimic.utilities.utilities module module mimic mimic.model_infer mimic.model_infer.cLV mimic.model_infer.infer_gMLV_lm mimic.model_infer.infer_VAR_bayes mimic.model_infer.multi_penalty_lasso mimic.model_simulate mimic.model_simulate.base_model mimic.model_simulate.sim_gMLV mimic.model_simulate.sim_VAR mimic.utilities mimic.utilities.utilities MultiPenaltyLasso (class in mimic.model_infer.multi_penalty_lasso)

N

non_zero_penalties() (mimic.model_infer.multi_penalty_lasso.MultiPenaltyLasso method)

P

penalised_lasso() (mimic.model_infer.multi_penalty_lasso.MultiPenaltyLasso method) plot_alpha_lasso() (in module mimic.model_infer.infer_gMLV_lm) plot_coeffs() (in module mimic.model_infer.infer_gMLV_lm) plot_fit_gLV() (in module mimic.utilities.utilities) plot_fit_gMLV() (in module mimic.utilities.utilities) plot_gLV() (in module mimic.utilities.utilities) plot_gMLV() (in module mimic.utilities.utilities)

plot_heatmap() (mimic.model_infer.infer_VAR_bayes.infer_VAR method) posterior_analysis() (mimic.model_infer.infer_VAR_bayes.infer_VAR method) predict() (in module mimic.model_infer.cLV) (mimic.model_infer.cLV.CompositionalLotkaVolterra method) (mimic.model_infer.infer_gMLV_lm.Ridge1 method) (mimic.model_infer.infer_gMLV_lm.Ridge2 method) (mimic.model_infer.multi_penalty_lasso.MultiPenaltyLasso method) print_parameters() (mimic.model_simulate.base_model.BaseModel method)

R

read_parameters() (in module mimic.utilities.utilities) (mimic.model_simulate.base_model.BaseModel method) Ridge1 (class in mimic.model_infer.infer_gMLV_lm) Ridge2 (class in mimic.model_infer.infer_gMLV_lm)

ridge_fit() (in module mimic.model_infer.infer_gMLV_lm) ridge_fit_pert() (in module mimic.model_infer.infer_gMLV_lm) ridge_fit_test() (in module mimic.model_infer.infer_gMLV_lm) ridge_regression_clv() (in module mimic.model_infer.cLV) run_inference() (mimic.model_infer.infer_VAR_bayes.infer_VAR method)

S

save_data() (mimic.model_simulate.base_model.BaseModel method) save_parameters() (mimic.model_simulate.base_model.BaseModel method) set_all_seeds() (in module mimic.utilities.utilities) set_parameters() (mimic.model_infer.infer_VAR_bayes.infer_VAR method) (mimic.model_simulate.base_model.BaseModel method) (mimic.model_simulate.sim_gMLV.sim_gMLV method) (mimic.model_simulate.sim_VAR.sim_VAR method) set_regularizers() (mimic.model_infer.cLV.CompositionalLotkaVolterra method)

set_score_request() (mimic.model_infer.infer_gMLV_lm.Ridge1 method) (mimic.model_infer.infer_gMLV_lm.Ridge2 method) (mimic.model_infer.multi_penalty_lasso.MultiPenaltyLasso method) sim_gMLV (class in mimic.model_simulate.sim_gMLV) sim_VAR (class in mimic.model_simulate.sim_VAR) simulate() (mimic.model_simulate.base_model.BaseModel method) (mimic.model_simulate.sim_gMLV.sim_gMLV method) (mimic.model_simulate.sim_VAR.sim_VAR method)

T

train() (mimic.model_infer.cLV.CompositionalLotkaVolterra method)

U

update_attributes() (mimic.model_simulate.base_model.BaseModel method)